pyEQL 1.4.0rc9__cp312-cp312-macosx_10_13_x86_64.whl

pyEQL/phreeqc/ext/iphreeqc-3.8.6-17100/doc/README

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+README
+
+        IPhreeqc--Modules Based on the Geochemical Model PHREEQC for Use
+                   in Scripting and Programming Languages
+        
+This file describes how to compile the IPhreeqc library and use
+it in C++, C, and Fortran programs. The library may be compiled
+after generating either a Visual Studio solution for Windows with 
+CMake or a Makefile for Linux with configure. All source and 
+compilation-related files are available at the following web site:
+
+http://wwwbrr.cr.usgs.gov/projects/GWC_coupled/phreeqc/index.html.
+
+-----------------------------------------------------------------------------------
+TABLE OF CONTENTS
+-----------------------------------------------------------------------------------
+
+	A. Distribution file
+	B. Documentation
+	C. Installing Windows COM versions
+	D. Downloading and unzipping the distribution file
+	E. Linux compiling, testing, and installing the IPhreeqc library
+	F. Windows compiling, testing, and installing the IPhreeqc library
+	G. Using the library
+	H. Contacts
+
+-----------------------------------------------------------------------------------
+A. Distribution file
+-----------------------------------------------------------------------------------
+
+	The following distribution packages (containing the software, 
+	compilation-related files, and an advection example in
+        C++, C, and Fortran) are available for Linux and Windows:
+
+        IPhreeqcCOM-3.8.6-17100-win32.msi  Windows
+        IPhreeqcCOM-3.8.6-17100-x64.msi    Windows
+        iphreeqc-3.8.6-17100.zip           Windows
+        iphreeqc-3.8.6-17100.tar.gz        Linux
+
+-----------------------------------------------------------------------------------
+B. Documentation
+-----------------------------------------------------------------------------------
+
+	Descriptions and examples of IPhreeqc methods for C++, C, and Fortran
+	are available in HTML format in the doc directory of the distribution. 
+
+	Charlton, S.R., and Parkhurst, D.L., 2011, Modules based on the geochemical model 
+	   PHREEQC for use in scripting and programming languages: Computers & Geosciences,
+	   vol. 37, no. 10, p. 1653-1663.
+
+	   *The following two user's guides are available in electronic format. Portable
+	   Document Format (PDF) files are included in the doc subdirectory of all
+	   PHREEQC program distributions.
+
+	Parkhurst, D.L., and Appelo, C.A.J., 2013, Description of input and examples
+	   for PHREEQC version 3--A computer program for speciation, batch-reaction,
+	   one- dimensional transport, and inverse geochemical calculations: U.S.
+	   Geological Survey Techniques and Methods, book 6, chap. A43, 497 p.
+	   http://pubs.usgs.gov/tm/06/a43/.
+
+	Parkhurst, D.L., and Appelo, C.A.J., 1999, User's guide to PHREEQC (Version
+	   2)-- A computer program for speciation, batch-reaction, one-dimensional
+	   transport, and inverse geochemical calculations: U.S. Geological Survey
+	   Water-Resources Investigations Report 99-4259, 312 p.
+	   http://pubs.er.usgs.gov/publication/wri994259.
+
+	   *The following two reports document the theory and implementation of
+	   isotopes in PHREEQC. Portable Document Format (PDF) of Thorstenson and
+	   Parkhurst (2002) is included in the doc subdirectory of the PHREEQC program
+	   distribution.
+
+	Thorstenson, D.C., and Parkhurst, D.L., 2002, Calculation of individual isotope
+	   equilibrium constants for implementation in geochemical models: U.S.
+	   Geological Survey Water-Resources Investigations Report 02-4172, 129 p.
+	   http://pubs.er.usgs.gov/publication/wri024172.
+
+	Thorstenson, D.C., and Parkhurst, D.L., 2004, Calculation of individual isotope
+	   equilibrium constants for geochemical reactions: Geochimica et Cosmochimica
+	   Acta, v. 68, no. 11, p. 2449-2465.
+
+	   *Brief description of the program PhreeqcI.
+
+	Charlton, S.R., and Parkhurst, D.L., 2002, PhreeqcI--A graphical user interface
+	   to the geochemical model PHREEQC: U.S. Geological Survey Fact Sheet
+	   FS-031-02, 2 p.
+
+-----------------------------------------------------------------------------------
+C. Installing Windows COM versions
+-----------------------------------------------------------------------------------
+	
+	For 64-bit computers, download both 32- and 64-bit versions:
+	
+	IPhreeqcCOM-3.8.6-17100-win32.msi  
+	IPhreeqcCOM-3.8.6-17100-x64.msi    	
+	
+	Double click on each .msi file and follow the instructions.
+	
+	IPhreeqcCOM is installed and ready to use for 32- and 64-bit applications.
+	
+	To test the COM, you can open the Excel file and run the "runphreeqc" macro 
+	(view->macros):
+	C:\Program Files\USGS\IPhreeqcCOM 3.2.0-9755\examples\com\excel\runphreeqc.xls
+	
+-----------------------------------------------------------------------------------
+D. Downloading and unzipping the distribution file
+-----------------------------------------------------------------------------------
+
+	Follow the steps using gunzip, 7zip, or other compression program that can unzip a tar.gz/zip file:
+
+	Steps in extracting files                       Explanation
+	----------------------------------------        -----------------------------------
+	gunzip iphreeqc-3.8.6-17100.tar.gz     Uncompress the tar.gz file.
+	tar -xvpof iphreeqc-3.8.6-17100.tar    Extract files from the tar file.
+
+	The directory iphreeqc-3.8.6-17100 is created when the files are
+	extracted; if this directory already exists, you may want to delete or rename
+	it before extracting the files. The following directory structure is created 
+	(the contents of each directory are shown to the right):
+
+	iphreeqc-3.8.6-17100                   Source code and configure/CMake files
+	     ./config                                   More configure files
+	     ./database                                 Database files for PHREEQC
+	     ./doc                                      Documentation files 
+	     ./examples                                 Advection example for Fortran, C++, and C
+	     ./src                                      Source code for IPhreeqc
+	     ./tests                                    Tests that check that C++, C, and Fortran(optional)
+                                                        are able to compile, link and run.
+
+	Note:  A compiled executable is not included in the distribution.
+
+-----------------------------------------------------------------------------------
+E. Linux compiling, testing, and installing the IPhreeqc library
+-----------------------------------------------------------------------------------
+
+	In general, to compile the software, you will need:
+
+		(a) a C++ compiler, and
+		(b) knowledge of configure, Make, 
+			the compiler, and the Linux operating system.
+
+	A Makefile is generated by configure, and the Makefile is used to
+	compile, test, and install the software.
+
+  E.1.  Change directory to the directory that was extracted from the tar file.
+
+        cd iphreeqc-3.8.6-17100
+        
+  E.2.  Make a directory, for example, build.
+	
+	mkdir build
+	
+  E.3.  Change directory to build.
+	
+	cd build
+
+  E.4.  Run configure
+
+	Many of the options for configure can be seen by typing:
+    
+    	../configure --help
+    
+	Most common options:
+    	--prefix=dir specifies the directory for installation of the
+    		library. Default is /usr/local, $HOME would install
+    		to your home directory.
+    	--enable-fortran-test=yes specifies that you do want to include the Fortran test
+    		files during "make check", which compiles, links, and runs programs 
+    		that use IPhreeqc.
+    		
+	Run configure as follows:	
+    	
+    	../configure [options] 
+
+  E.5.  Compile the IPhreeqc library
+	
+	make [-j 4]
+	
+    	Optionally, use -j n--where n is the number of compilations make runs in parallel.
+	
+  E.6.  Compile and run the test cases. The files in the directory tests are compiled
+	and linked to the IPhreeqc library. The Fortran files are optionally included
+	(--enable-fortran-test configure option).
+	
+	make check
+	
+  E.7.  Install the IPhreeqc library. By default the program is installed in /usr/local/bin
+	and /usr/local/share/doc/iphreeqc. Alternatively, the directory defined by --prefix
+	in the configure command is used. 
+    
+    	make install
+    	
+	The locations of various files are given for default installation (no
+	--prefix definition). 
+    
+	Libraries:
+		/usr/local/lib/libiphreeqc.a            (Static library)
+		/usr/local/lib/libiphreeqc.so           (Shared object library)
+		/usr/local/lib/libiphreeqc.la           (libtool library file)
+		    
+	Include files:
+		C++ and C headers for user's code:
+		/usr/local/include/IPhreeqc.h           (C header)
+		/usr/local/include/IPhreeqc.hpp         (C++ header)
+		
+		Optionally, user's code may need one or more of the following:
+		/usr/local/include/Var.h                
+		/usr/local/include/IPhreeqcCallbacks.h  
+		/usr/local/include/Keywords.h
+		/usr/local/include/PHRQ_io.h
+	
+	Documentation:
+		/usr/local/share/doc/iphreeqc/IPhreeqc.pdf
+		/usr/local/share/doc/iphreeqc/html/index.html (IPhreeqc API)
+		/usr/local/share/doc/iphreeqc/RELEASE (Release notes)
+		/usr/local/share/doc/iphreeqc/README (this readme file)
+		/usr/local/share/doc/iphreeqc/NOTICE (User rights notice)
+
+	Databases: 
+		/usr/local/share/doc/iphreeqc/database
+			  Amm.dat
+			  ColdChem.dat
+			  core10.dat
+			  frezchem.dat
+			  iso.dat
+			  llnl.dat
+			  minteq.dat
+			  minteq.v4.dat
+			  phreeqc.dat
+			  pitzer.dat
+			  sit.dat
+			  Tipping_Hurley.dat
+			  wateq4f.dat
+		
+	Advection example for Fortran, C++, and C: 
+		/usr/local/share/doc/iphreeqc/examples
+		
+	Fortran interface
+		/usr/local/share/doc/iphreeqc/src/IPhreeqc_interface.F90
+			
+    
+-----------------------------------------------------------------------------------
+F. Windows compiling, testing, and installing the IPhreeqc library
+-----------------------------------------------------------------------------------
+
+	In general, to compile the IPhreeqc library, you will need:
+
+		(a) CMake (build process manager)
+		(b) a C++ compiler,
+		(c) familiarity with the compiler and the Windows operating system.
+   
+  F.1. Download and install CMake
+
+	CMake can be downloaded from http://www.cmake.org/. If you download
+	the executable, CMake is installed when you execute it.
+
+  F.2  Generate a Visual Studio solution
+
+	CMake has many options other than Visual Studio, but here we assume
+	that you are using some version of Visual Studio. On the first use
+	of CMake, it may be necessary to close all Visual Studio instances. 
+	
+	Open CMake. Fill in the top two lines.
+		Where is the source code: 
+			The top level directory (ie c:/iphreeqc-3.8.6-17100).
+		Where to build the binaries: 
+			A new directory. It is suggested that the name
+			of the directory include the characteristics of 
+			the library that is built, including the VS
+			version, 32/64 bit, dll/lib.
+			for example, vs2012_64_dll.
+	
+	Click Configure. From the pulldown menu select the 64-bit version 
+	for your Visual Studio. Normally, the default radio button should
+	be sufficient. Click Finish. 
+	
+	Options in the top panel:
+	(1) BUILD_SHARED_LIBS--If checked, .dll files will be
+		created. If not checked, a .lib file will be created.
+		Note that .dll files have a .lib file associated with them,
+		but it is not the same .lib generated when
+		BUILD_SHARED_LIBS is not checked.
+	(2) CMAKE_INSTALL_PREFIX--Sets the the install directory where the 
+		library and header files will be saved. It is suggested that
+		an INSTALL directory be defined inside the directory chosen 
+		for the binaries.
+	(3) BUILD_CLR_LIBS--If checked, will compile the CLR version of the
+	        library. This will enable the charting capabilities of
+	        phreeqc through the use of Zedgraph.  This option is only
+	        available if BUILD_SHARED_LIBS is checked.
+	(4) IPHREEQC_ENABLE_MODULE--Uncheck if you want to
+		use the deprecated (old-style) include file (IPhreeqc.f90.inc 
+		or IPhreeqc.f.inc) to define IPhreeqc in Fortran files.
+		Leave checked to use IPhreeqc as a Fortran module (USE IPhreeqc), 
+		which is recommended. Leave checked if not using Fortran. 
+	(5) IPHREEQC_FORTRAN_TESTING--Sets whether the test calculations
+		(tests directory) will include Fortran test files. A Fortran
+		compiler is required. 
+	
+	Click Configure until the screen is not red. If the screen remains 
+	red, you will have to deal with the CMake error messages.
+	
+	Click Generate.
+	
+	You should now have a Visual Studio solution file (.sln) in the 
+	directory chosen for the binaries (second line of CMake screen). 
+	At any point, you can delete the contents of the directory and
+	start over. You can make solutions for different Visual Studios,
+	or different options in other directories.
+	
+  F.3. Compile and install IPhreeqc
+
+	Open the Visual Studio solution in the build directory defined in CMake.
+	
+	The default configuration is "Debug". If you want a release libraries
+	(or dlls) and examples,	change the configuration to "Release".
+
+	Build ALL_BUILD. IPhreeqc is compiled.
+
+	Build RUN_TESTS. Programs that test IPhreeqc are compiled and run, 
+	and optionally (CMake IPHREEQC_FORTRAN_TESTING option) the Fortran test
+	project. 
+	
+
+	Build INSTALL. The libraries, header files, Fortran module source
+	files, phreeqc database files, and documentation are installed in the
+	install directory selected in CMake.
+
+		Install\library directory (lib or dll) may include:
+			IPhreeqc.lib       (Release)
+			IPhreeqcd.lib      (Debug)
+			IPhreeqcmsr.lib    (MinSizeRel)
+			IPhreeqcrwdi.lib   (RelWithDebInfo)
+			IPhreeqc.dll       (Release Shared)
+			IPhreeqcd.dll      (Debug Shared)
+			IPhreeqcmsr.dll    (MinSizeRel Shared)
+			IPhreeqcrwdi.dll   (RelWithDebInfo Shared)		
+			ZedGraph.dll       (CLR/Charting)
+
+		Install\include files:
+			C++ and C headers for user's code:	
+				IPhreeqc.hpp         (C++ header)
+				IPhreeqc.h           (C header)
+
+			Optionally, you may need one or more of the following:
+				Var.h                
+				IPhreeqcCallbacks.h  
+				Keywords.h
+				PHRQ_io.h
+
+		Install\src files:
+			To use IPhreeqc in Fortran:
+				IPhreeqc_interface.F90
+
+		Install\Database files:
+			Amm.dat
+			frezchem.dat
+			iso.dat
+			llnl.dat
+			minteq.dat
+			minteq.v4.dat
+			phreeqc.dat
+			pitzer.dat
+			sit.dat
+			wateq4f.dat
+				
+		Install\doc files:
+			IPhreeqc.pdf          IPhreeqc journal article
+			html\index.html       IPhreeqc API documentation
+			NOTICE                User rights notice 
+			README                This readme file
+			RELEASE               Release notes
+
+		Install\examples files:
+			c, cpp, fortran       Advection example
+
+
+	Note: In order to use the CLR version (Charting) the Zedgraph.dll file
+	must be registered either by installing the Phreeqc or the PhreeqcI MSI,
+	or through the use of the Visual Studio Tool gacutil.
+
+-----------------------------------------------------------------------------------        			
+G. Using the library
+-----------------------------------------------------------------------------------
+
+  G.1. C++
+     
+     In C++, you will include the IPhreeqc.hpp header file and 
+     create an IPhreeqc instance:
+
+     #include "IPhreeqc.hpp"
+     IPhreeqc iphreeqc;
+
+     or
+
+     IPhreeqc *iphreeqc = new IPhreeqc();
+
+     You will need to link to the IPhreeqc.lib that you installed.
+
+  G.2. C
+
+     In C, you will include the C interface header, IPhreeqc.h, and
+     create an IPhreeqc instance.
+
+     #include "IPhreeqc.h"
+     int id;
+     id = CreateIPhreeqc();
+
+     You will need to link to the IPhreeqc.lib that you installed.
+
+  G.3. Fortran
+
+     In Fortran, you will need to include the source file IPhreeqc_interface.F90
+     in your project files. This file defines the IPhreeqc Fortran module.
+
+     USE IPhreeqc
+     INTEGER(KIND=4) id
+     id = CreateIPhreeqc()
+
+     You will need to link to the IPhreeqc.lib that you installed.
+
+-----------------------------------------------------------------------------------
+H. CONTACTS
+-----------------------------------------------------------------------------------
+
+Inquiries about this software distribution should be directed to:
+
+e-mail:  h2osoft@usgs.gov or dlpark@usgs.gov
+